If you're seeing this, something is embarrassingly wrong

[jeremyjyang]

Category: FYI/WTF.

Got this error message yesterday (3/15). "Beware the ides of March." comes to mind...

Loading all CV terms used in submission tables... [Tue 15 Mar 2022 09:37:48 AM MDT]

scanning "/home/data/CFDE/data/targetpages6124/submission/file.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/biosample.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/biosample_disease.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/biosample_gene.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/biosample_substance.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/subject_disease.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/subject_role_taxonomy.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/subject_substance.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/collection_disease.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/phenotype_disease.tsv"...
scanning "/home/data/CFDE/data/targetpages6124/submission/phenotype_gene.tsv"...

...done scanning all CV terms used in this submission. [Tue 15 Mar 2022 09:37:48 AM MDT]
Loading display data (names, descriptions, etc.) for all CV terms used in submission tables... [Tue 15 Mar 2022 09:37:49 AM MDT]

Uber-anatomy ontology... [Tue 15 Mar 2022 09:37:49 AM MDT]
Ontology for Biomedical Investigations (assay type)... [Tue 15 Mar 2022 09:37:50 AM MDT]
Ontology for Biomedical Investigations (analysis type)... [Tue 15 Mar 2022 09:37:50 AM MDT]
EDAM (data type)... [Tue 15 Mar 2022 09:37:50 AM MDT]
Disease Ontology... [Tue 15 Mar 2022 09:37:50 AM MDT]
EDAM (file format)... [Tue 15 Mar 2022 09:37:51 AM MDT]
NCBI Taxonomy... [Tue 15 Mar 2022 09:37:51 AM MDT]
Ensembl genes... [Tue 15 Mar 2022 09:37:57 AM MDT]
PubChem substances and compounds [if you included PubChem terms in your submission, this step will take around 10 minutes, even with a fast disk]...
...processing substance file... [Tue 15 Mar 2022 09:37:57 AM MDT]
...processing compound file... [Tue 15 Mar 2022 09:37:58 AM MDT]

...done loading display data for all CVs. [Tue 15 Mar 2022 09:37:58 AM MDT]
Writing CV term tracker tables (to be included in complete C2M2 submission)... [Tue 15 Mar 2022 09:37:58 AM MDT]

writing "/home/data/CFDE/data/targetpages6124/submission/anatomy.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/assay_type.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/analysis_type.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/data_type.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/disease.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/file_format.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/ncbi_taxonomy.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/gene.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/substance.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
writing "/home/data/CFDE/data/targetpages6124/submission/compound.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]

...done writing term tables for final C2M2 submission datapackage. [Tue 15 Mar 2022 09:37:58 AM MDT]
NOTE: HPO phenotype data processing is currently offline; stubs will be generated for basic format compliance, but non-null phenotype code values will be ignored and may cause submission errors.
Writing "/home/data/CFDE/data/targetpages6124/submission/phenotype.tsv"... [Tue 15 Mar 2022 09:37:58 AM MDT]
Ensuring all file.tsv records with persistent IDs have non-null checksums... [Tue 15 Mar 2022 09:37:58 AM MDT]

...done; all file records passed checksum verification. [Tue 15 Mar 2022 09:37:59 AM MDT]
Ensuring all persistent IDs are unique (both within and across tables)... [Tue 15 Mar 2022 09:37:59 AM MDT]

FATAL: If you're seeing this, something is embarrassingly wrong

[abradyIGS]

Changed error message to "If you're seeing this, you're missing a required persistent_id column in one or more of file.tsv, biosample.tsv, subject.tsv, collection.tsv or project.tsv," which is what it should've said all along -- sorry for crypticity.

Please check for required persistent_id column in all listed tables (values can be null, but column must be present); if it's there in all of them, please send copies of all five tables, as parsing will have failed in an unknown manner